Perhaps the biggest differentiator between otherwise good quality flash units is the extent of their master / slave functionality. The most functional are those that support full E-TTL II auto exposure in a wireless master / slave set-up. Canon's units obviously do this (580EX II as master or slave, 430EX II as slave only). Other current units that do this are the Nissin Di866 MkII and Sigma EF610 DG Super (both as either master or slave), plus the Metz 58 AF-2, Nissin Di622 MkII and Yongnuo 565EX (all as slave only).
The third party units supposedly use the same (optical) wireless communication system as the Canons so they should all be able to talk to each other. I can't verify this as mine is an all-Sigma system. Obviously, none of the above will communicate by radio frequency with Canon's 600EX-RT but that unit does also have the optical system for backward compatibility.